VCV002499613.2 - ClinVar

NM_001375524.1(TRRAP):c.5816C>T (p.Pro1939Leu)

Germline

Classification

criteria provided, single submitter. Learn more about how ClinVar calculates review status.

Likely pathogenic

This classification is based on the single submission received

The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_001375524.1(TRRAP):c.5816C>T (p.Pro1939Leu)

Variation ID: 2499613 Accession: VCV002499613.2

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: 7q22.1 7: 98955183 (GRCh38) [ NCBI UCSC ] 7: 98552806 (GRCh37) [ NCBI UCSC ]

Timeline in ClinVar

	First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.	Last submission Help The date of the most recent submission for each type of classification for this variant.	Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline	Apr 30, 2023	Apr 30, 2023	Apr 20, 2023

HGVS

Nucleotide	Protein	Molecular consequence
NM_001375524.1:c.5816C>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_001362453.1:p.Pro1939Leu	missense
NM_001244580.2:c.5795C>T	NP_001231509.1:p.Pro1932Leu	missense
NM_003496.4:c.5741C>T	NP_003487.1:p.Pro1914Leu	missense
NC_000007.14:g.98955183C>T
NC_000007.13:g.98552806C>T
NG_030010.1:g.81694C>T

... more HGVS ... less HGVS

Protein change

P1914L, P1932L, P1939L

Other names

Canonical SPDI

NC_000007.14:98955182:C:T

Functional consequence Help The effect of the variant on RNA or protein function, based on experimental evidence from submitters.

Global minor allele frequency (GMAF) Help The global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.

Allele frequency Help The frequency of the allele represented by this VCV record.

Links

ClinGen: CA368323349 VarSome

Genes

Gene	OMIM	ClinGen Gene Dosage Sensitivity Curation		Variation Viewer Help Links to Variation Viewer, a genome browser to view variation data from NCBI databases.	Related variants
Gene	OMIM	HI score Help The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.	TS score Help The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.		Within gene Help The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants.	All Help The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene.
TRRAP		Little evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	2106	2198

Conditions - Germline

Condition Help The condition for this variant-condition (RCV) record in ClinVar.	Classification Help The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions)	Review status Help The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status.	Last evaluated Help The most recent date that a submitter evaluated this variant for the condition.	Variation/condition record Help The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page.
Developmental delay with or without dysmorphic facies and autism	Likely pathogenic (1)	criteria provided, single submitter	Apr 20, 2023	RCV003223542.2

Submissions - Germline

Classification Help The submitted germline classification for each SCV record. (Last evaluated)	Review status Help Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria)	Condition Help The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant.	Submitter Help The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar.	More information Help This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter.
Likely pathogenic (Apr 20, 2023) C Contributing to aggregate classification	criteria provided, single submitter (ACMG Guidelines, 2015) Method: research	Developmental delay with or without dysmorphic facies and autism Affected status: yes Allele origin: maternal	Duke University Health System Sequencing Clinic, Duke University Health System Accession: SCV003919077.1 First in ClinVar: Apr 30, 2023 Last updated: Apr 30, 2023	Publications: PubMed (1) PubMed: 30827496

Germline Functional Evidence

There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for germline classification of this variant

Title	Author	Journal	Year	Link
Missense Variants in the Histone Acetyltransferase Complex Component Gene TRRAP Cause Autism and Syndromic Intellectual Disability.	Cogné B	American journal of human genetics	2019	PMID: 30827496

Text-mined citations for this variant ...

Record last updated May 07, 2023

ClinVar Genomic variation as it relates to human health

NM_001375524.1(TRRAP):c.5816C>T (p.Pro1939Leu)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...